Source Code for Module test_suite.unit_tests._lib._dispersion.test_ns_cpmg_2site_3d

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2014 Edward d'Auvergne                                        # 
  4  # Copyright (C) 2014 Troels E. Linnet                                         # 
  5  #                                                                             # 
  6  # This file is part of the program relax (http://www.nmr-relax.com).          # 
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 19  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
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 21  ############################################################################### 
 22   
 23  # Python module imports. 
 24  from numpy import array, float64, ones, pi, rollaxis, zeros 
 25  from unittest import TestCase 
 26   
 27  # relax module imports. 
 28  from lib.dispersion.ns_cpmg_2site_3d import r2eff_ns_cpmg_2site_3D 
 29  from lib.dispersion.ns_matrices import r180x_3d 
 30   
 31   
 32 -class Test_ns_cpmg_2site_3d(TestCase): 
 33      """Unit tests for the lib.dispersion.ns_cpmg_2site_3D relax module.""" 
 34   
 35 -    def setUp(self): 
 36          """Set up for all unit tests.""" 
 37   
 38          # Default parameter values. 
 39          self.r20a = 2.0 
 40          self.r20b = 3.0 
 41          self.pA = 0.95 
 42          self.dw = 2.0 
 43          self.kex = 1000.0 
 44   
 45          # Required data structures. 
 46          # The 3D rotation matrix for an imperfect X-axis pi-pulse. 
 47          self.r180x = r180x_3d() 
 48   
 49          self.num_points = 7 
 50          self.ncyc = array([2, 4, 8, 10, 20, 40, 500]) 
 51          relax_times = 0.04 
 52          cpmg_frqs = self.ncyc / relax_times 
 53          self.inv_relax_times = 1.0 / relax_times 
 54          self.tau_cpmg = 0.25 / cpmg_frqs 
 55   
 56          self.array_shape = [1, 1, 1, 1, self.num_points] 
 57          self.R2eff = zeros(self.num_points, float64) * ones(self.array_shape) 
 58   
 59          # The spin Larmor frequencies. 
 60          self.sfrq = 200. * 1E6 
 61   
 62          # This is a vector that contains the initial magnetizations corresponding to the A and B state transverse magnetizations. 
 63          M0_0 = zeros( [1, 1, 1, 1, 1, 7, 1], float64) 
 64          M0_0[:, :, :, :, :, 0, 0] = 0.5 
 65          self.M0 = M0_0 
 66          # Transpose M0, to prepare for dot operation. Roll the last axis one back, corresponds to a transpose for the outer two axis. 
 67          self.M0_T = rollaxis(self.M0, 6, 5) 
 68   
 69   
 70 -    def calc_r2eff(self): 
 71          """Calculate and check the R2eff values.""" 
 72   
 73          # Parameter conversions. 
 74          k_AB, k_BA, pB, dw_frq = self.param_conversion(pA=self.pA, kex=self.kex, dw=self.dw, sfrq=self.sfrq) 
 75   
 76          a = ones(self.array_shape) 
 77          b = ones([1, 1, 1, 1]) 
 78   
 79          # Calculate the R2eff values. 
 80          r2eff_ns_cpmg_2site_3D(r180x=self.r180x, M0=self.M0, M0_T=self.M0_T, r20a=self.r20a*a, r20b=self.r20b*a, pA=self.pA, dw=dw_frq*a, dw_orig=dw_frq*a, kex=self.kex, inv_tcpmg=self.inv_relax_times*a, tcp=self.tau_cpmg*a, back_calc=self.R2eff, num_points=self.num_points*b, power=self.ncyc*a) 
 81   
 82          if self.kex >= 1.e5: 
 83              for i in range(self.num_points): 
 84                  self.assertAlmostEqual(self.R2eff[0][0][0][0][i], self.r20a, 5) 
 85          else: 
 86              for i in range(self.num_points): 
 87                  self.assertAlmostEqual(self.R2eff[0][0][0][0][i], self.r20a) 
 88   
 89   
 90 -    def param_conversion(self, pA=None, kex=None, dw=None, sfrq=None): 
 91          """Convert the parameters. 
 92   
 93          @keyword pA:    The population of state A. 
 94          @type pA:       float 
 95          @keyword kex:   The rate of exchange. 
 96          @type kex:      float 
 97          @keyword dw:    The chemical exchange difference between states A and B in ppm. 
 98          @type dw:       float 
 99          @keyword sfrq:  The spin Larmor frequencies in Hz. 
100          @type sfrq:     float 
101          @keyword M0:    Vector that contains the initial magnetizations corresponding to the A and B state transverse magnetizations. 
102          @type M0:       numpy float64, rank-1, 7D array 
103          @return:        The parameters {k_AB, k_BA, pB, dw_frq, M0}. 
104          @rtype:         tuple of float 
105          """ 
106   
107          # Calculate pB. 
108          pB = 1.0 - pA 
109   
110          # Exchange rates. 
111          k_BA = pA * kex 
112          k_AB = pB * kex 
113   
114          # Calculate spin Larmor frequencies in 2pi. 
115          frqs = sfrq * 2 * pi 
116   
117          # Convert dw from ppm to rad/s. 
118          dw_frq = dw * frqs / 1.e6 
119   
120          # Return all values. 
121          return k_AB, k_BA, pB, dw_frq 
122   
123   
124 -    def test_ns_cpmg_2site_3D_no_rex1(self): 
125          """Test the r2eff_ns_cpmg_2site_3D() function for no exchange when dw = 0.0.""" 
126   
127          # Parameter reset. 
128          self.dw = 0.0 
129   
130          # Calculate and check the R2eff values. 
131          self.calc_r2eff() 
132   
133   
134 -    def test_ns_cpmg_2site_3D_no_rex2(self): 
135          """Test the r2eff_ns_cpmg_2site_3D() function for no exchange when pA = 1.0.""" 
136   
137          # Parameter reset. 
138          self.pA = 1.0 
139   
140          # Calculate and check the R2eff values. 
141          self.calc_r2eff() 
142   
143   
144 -    def test_ns_cpmg_2site_3D_no_rex3(self): 
145          """Test the r2eff_ns_cpmg_2site_3D() function for no exchange when kex = 0.0.""" 
146   
147          # Parameter reset. 
148          self.kex = 0.0 
149   
150          # Calculate and check the R2eff values. 
151          self.calc_r2eff() 
152   
153   
154 -    def test_ns_cpmg_2site_3D_no_rex4(self): 
155          """Test the r2eff_ns_cpmg_2site_3D() function for no exchange when dw = 0.0 and pA = 1.0.""" 
156   
157          # Parameter reset. 
158          self.pA = 1.0 
159          self.dw = 0.0 
160   
161          # Calculate and check the R2eff values. 
162          self.calc_r2eff() 
163   
164   
165 -    def test_ns_cpmg_2site_3D_no_rex5(self): 
166          """Test the r2eff_ns_cpmg_2site_3D() function for no exchange when dw = 0.0 and kex = 0.0.""" 
167   
168          # Parameter reset. 
169          self.dw = 0.0 
170          self.kex = 0.0 
171   
172          # Calculate and check the R2eff values. 
173          self.calc_r2eff() 
174   
175   
176 -    def test_ns_cpmg_2site_3D_no_rex6(self): 
177          """Test the r2eff_ns_cpmg_2site_3D() function for no exchange when pA = 1.0 and kex = 0.0.""" 
178   
179          # Parameter reset. 
180          self.pA = 1.0 
181          self.kex = 0.0 
182   
183          # Calculate and check the R2eff values. 
184          self.calc_r2eff() 
185   
186   
187 -    def test_ns_cpmg_2site_3D_no_rex7(self): 
188          """Test the r2eff_ns_cpmg_2site_3D() function for no exchange when dw = 0.0, pA = 1.0, and kex = 0.0.""" 
189   
190          # Parameter reset. 
191          self.dw = 0.0 
192          self.kex = 0.0 
193   
194          # Calculate and check the R2eff values. 
195          self.calc_r2eff() 
196